Mask entries in simulated SFS out if they are negative #663
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # This is a basic workflow to help you get started with Actions | |
| name: build | |
| # Controls when the action will run. Triggers the workflow on push or pull request | |
| # events but only for the master branch | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, windows-2019, macos-latest] | |
| python-version: [3.6, 3.8] | |
| include: | |
| - os: windows-2019 | |
| triplet: x64-windows | |
| env: | |
| CONDA_ENV_NAME: gadma_env | |
| steps: | |
| - name: Cancel previous runs. | |
| uses: styfle/cancel-workflow-action@0.6.0 | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout. | |
| uses: actions/checkout@v2 | |
| - name: Set up Python 3. | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install minimal requirements before everything else | |
| run: | | |
| pip3 install -r requirements/minimal.txt | |
| # - name: Install conda (Windows) | |
| # if: runner.os == 'Windows' && matrix.python-version == '3.8' | |
| # uses: conda-incubator/setup-miniconda@v2 | |
| # with: | |
| # python-version: ${{ matrix.python }} | |
| # channels: conda-forge, r, bioconda | |
| # #channel-priority: strict | |
| # auto-update-conda: true | |
| # use-only-tar-bz2: true | |
| # | |
| # # For future, to check msprime versions: conda search msprime --info | |
| # - name: Install msprime via conda (Windows python3.8) | |
| # if: runner.os == 'Windows' && matrix.python-version == '3.8' | |
| # shell: bash -l {0} #We need a login shell to get conda | |
| # run: | | |
| # # We install msprime from conda to avoid GSL-related build issues | |
| # # when pip installing without binary wheels (on Windows). | |
| # # We install a special version of msprime 0.7.4=py36 | |
| # #conda activate ${{ env.CONDA_ENV_NAME }} | |
| # conda create -n ${{ env.CONDA_ENV_NAME }} msprime python=${{ matrix.python-version }} | |
| - name: Install hdf5, msprime and momi2 (MacOS). | |
| run: | | |
| brew install gsl homebrew/core/hdf5 | |
| pip3 install msprime | |
| brew install libomp llvm | |
| export LDFLAGS="-L/usr/local/opt/llvm/lib" | |
| export CPPFLAGS="-I/usr/local/opt/llvm/include" | |
| CC=$(brew --prefix llvm)/bin/clang pip install momi | |
| if: matrix.os == 'macos-10.15' | |
| # - name: Install GADMA and its dependencies (Windows python3.8). | |
| # if: runner.os == 'Windows' && matrix.python-version == '3.8' | |
| # shell: bash -l {0} | |
| # run: | | |
| # conda activate ${{ env.CONDA_ENV_NAME }} | |
| # bash install | |
| # pip3 install -r requirements/bayes_opt.txt | |
| - name: Install GADMA and its dependencies. | |
| run: | | |
| bash install | |
| pip3 install -r requirements/bayes_opt.txt | |
| pip3 install -r requirements/bayes_opt_addit.txt | |
| - name: Uninstall SMAC (Windows). | |
| if: runner.os == 'Windows' | |
| shell: bash -l {0} | |
| run: | | |
| pip3 uninstall -y smac | |
| - name: Install momentsLD engine. | |
| run: | | |
| pip3 uninstall -y moments | |
| pip3 install Cython==0.29.18 # the last version cause erros on Windows and MacOS | |
| git clone --depth 1 --branch moments-1.1.11 https://bitbucket.org/simongravel/moments.git | |
| cd moments | |
| pip install -r requirements.txt | |
| python3 setup.py build_ext --inplace | |
| python3 setup.py install | |
| cd .. | |
| # For some reason the last version of wheel cause an error for momi installation | |
| - name: Use specific version of wheel for momi installation (Linux) | |
| if: runner.os == 'Linux' && matrix.python-version == '3.8' | |
| run: | | |
| python3 -m pip install wheel==0.38.4 | |
| - name: Install momi engine (Linux). | |
| if: runner.os == 'Linux' | |
| run: | | |
| python3 -m pip install momi | |
| - name: Check installations of packages. | |
| run: | | |
| python3 -c "import numpy" | |
| python3 -c "import scipy" | |
| python3 -c "import dadi" | |
| python3 -c "import moments" | |
| python3 -c "import gadma" | |
| - name: Show versions of all installed packages. | |
| run: python3 -m pip freeze | |
| - name: Show available engines and optimizations in gadma. | |
| run: | | |
| python3 -c "import gadma;print(gadma.engines.engine._registered_engines.keys())" | |
| python3 -c "import gadma;print(gadma.optimizers.global_optimizer._registered_global_optimizers.keys())" | |
| - name: Install dependencies for tests. | |
| run: | | |
| pip3 install -r requirements/tests.txt | |
| - name: Run tests and codecov. | |
| run: | | |
| pytest --timeout=400 --cov=gadma --cov-report=xml -v tests --disable-warnings | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| if: matrix.os == 'ubuntu-18.04' && matrix.python-version == '3.6' | |